Evidence map›Paper›PMID 39992132›Full record

ArticlemSystems2025

Environmental matrix and moisture influence soil microbial phenotypes in a simplified porous media incubation.

Josué Rodríguez-Ramos, Natalie Sadler, Elias K Zegeye, Yuliya Farris, Samuel Purvine, Sneha Couvillion, William C Nelson, Kirsten S Hofmockel

Abstract read
In one paragraph

Article in mSystems, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.

0numbers the graph read from it
0cells of the map it votes in
3citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

3 citing papers in PubMed.

  1. Article
  2. Article
  3. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

8 authors.

Josué Rodríguez-Ramos *Pacific Northwest National Laboratory, Earth and Biological Sciences Directorate, Richland, Washington, USA.ORCID 0000-0002-2049-2765
Natalie Sadler *Pacific Northwest National Laboratory, Earth and Biological Sciences Directorate, Richland, Washington, USA.ORCID 0000-0003-1161-5687
Elias K ZegeyePacific Northwest National Laboratory, Earth and Biological Sciences Directorate, Richland, Washington, USA.ORCID 0000-0002-5130-582X
Yuliya FarrisPacific Northwest National Laboratory, Earth and Biological Sciences Directorate, Richland, Washington, USA.
Samuel PurvinePacific Northwest National Laboratory, Earth and Biological Sciences Directorate, Richland, Washington, USA.ORCID 0000-0002-2257-2400
Sneha CouvillionPacific Northwest National Laboratory, Earth and Biological Sciences Directorate, Richland, Washington, USA.ORCID 0000-0003-0307-9343
William C NelsonPacific Northwest National Laboratory, Earth and Biological Sciences Directorate, Richland, Washington, USA.ORCID 0000-0002-1873-3929
Kirsten S HofmockelPacific Northwest National Laboratory, Earth and Biological Sciences Directorate, Richland, Washington, USA.ORCID 0000-0003-1586-2167

Funding

Department of Energy, Office of Science, Genomic Sciences Program FWP 70880DOE | SC | PNNL | Environmental Molecular Sciences Laboratory (EMSL) 60461Joint Genome Institute (JGI) 508623
6 · The paper itself

Abstract

Soil moisture and porosity regulate microbial metabolism by influencing factors, such as system chemistry, substrate availability, and soil connectivity. However, accurately representing the soil environment and establishing a tractable microbial community that limits confounding variables is difficult. Here, we use a reduced-complexity microbial consortium grown in a glass bead porous media amended with chitin to test the effects of moisture and a structural matrix on microbial phenotypes. Leveraging metagenomes, metatranscriptomes, metaproteomes, and metabolomes, we saw that our porous media system significantly altered microbial phenotypes compared with the liquid incubations, denoting the importance of incorporating pores and surfaces for understanding microbial phenotypes in soils. These phenotypic shifts were mainly driven by differences in expression of

Indexed as

SoilSoil MicrobiologyChitinMetabolomeMetagenomeMicrobial ConsortiaMicrobiotaPhenotypePorosityStreptomycesWaterChitinSoilWatercarbon use efficiencychitin metabolismglyoxylate shuntmetagenomicsmetaproteomicsmetatranscriptomicsmicrobial stress responsemodel soil microbial communitysoil microbiologysoil moisture

Identifiers

PMID39992132
PMCPMC11915792

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.